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Thermo Fisher Scientific, Ion S5 and Ion S5 XL Systems

Thermo Fisher Scientific, Ion S5 and Ion S5 XL Systems

Next-generation sequencing instruments, December 2017

Contact Information

Thermo Fisher Scientific
Mauricio Minotta
5791 Van Allen Way
Carlsbad, CA 92008

Name of instrument Ion S5 and Ion S5 XL Systems
Name of model/Model has been upgraded —/no
Country where designed/Manufactured/FDA cleared or approved U.S./U.S./not required
First year sold in U.S./Outside U.S./First year installed 2015/2015/2015
Dimensions in inches (H × W × D)/Footprint of all instrumentation and computing hardware 20 × 21.4 × 31.8/7.2 square feet
Equipment supplied with system/Automation for library preparation Ion S5 Sequencer/yes
Necessary equipment not included with system and additional cost general laboratory supplies
Bioinformatics tools provided/For use by biologist or bioinformatician Ion Reporter, Torrent Suite software, Torrent Circuit/biologist
Supplied with UPS/Entire workflow can occur in same lab no/yes
Clean room requirements/Electrical connection none/100–240 V, 14.5 A, 5060 Hz, 1350 W
List price/Total list price for equipment needed to perform simplest and fastest workflow from amplification through variant calling (not typically found in lab) Ion S5: $65,000; Ion S5 XL: $150,000/$120,000–$170,000
Purchase options purchase or lease (financing available)
Warranties offered 1 year included, extended warranty available
Training included/Total time for standard install and basic training yes/1 day
Training location/Follow-up training available on and off site/yes, extra charge
Instrument core performance:
Maximum No. of libraries amplified in single amplification event 384, with custom barcodes
Read length/Percent bases >Q30 up to 400 bp/—
Paired-end capability/Tag lengths/Spans
Fragment/Tag lengths/Spans yes/—/up to 400 bp
Mate-pair/Tag lengths/Spans yes/—/—
Single-end/Tag lengths/Spans yes/—/up to 400 bp
RNA sequencing/Tag lengths/Spans yes/—/up to 400 bp
ChIP sequencing/Tag lengths/Spans
Bisulfite sequencing/Tag lengths/Spans
Output per run 0.6–2 Gb (Ion 520 chip), 3–8 Gb (Ion 530 chip), 10–15 Gb (Ion 540 chip)
Total time from library construction to variant calling to achieve output per run/Technical bench time/Bioinformatics time <24 hours/<45 minutes/<1 hour
Sample preparation:
Total time for generating standard gDNA library varies
• Paired-end
• Fragment 4–6 hours
• Mate-pair 2.5 days
• Single-end 5–7 hours
• RNA sequencing <6 hours
• ChIP sequencing customer demonstrated
• Bisulfite sequencing customer demonstrated
Hands-on time each:
• Paired-end
• Fragment 1 hour
• Mate-pair 6 hours
• Single-end 15 minutes
• RNA sequencing 1 hour with Ion AmpliSeq Transcriptome
• ChIP sequencing
• Bisulfite sequencing
Equipment required for library construction Ion Chef System for Ion AmpliSeq libraries, standard laboratory equipment
Reagents and controls:
Cost per run $928 (Ion 520 chip), $1,088 (Ion 530 chip), $1,250 (Ion 540 chip)
Cost per sample* varies
Reagent tracking method on instrument RFID
Information contained in tracking method expiration date, lot number, part number
Reagent shipping conditions/Storage conditions -20°C, 4°C, and ambient/-20°C, 4°C, and ambient
Shelf life of amplification and sequencing reagents varies
Controls introduced during creation of library/Sequencing control avail. yes/yes
Capable of complete walkaway automation for amplification, sequencing, and variant calling yes
Remote system monitoring yes
Instrument control software and devices to start run/for data analysis Torrent Suite Software/Torrent Suite Software, Ion Reporter Software
Total time required for setup of amplification, sequencing, and variant calling steps <30 minutes
Maximum No. of libraries sequenced in a single run 384
Types of maintenance plans available AB Assurance, AB Complete, AB Maintenance Plus, AB Maintenance Service
No. of field apps scientists and engineers based in U.S.
Weekly maintenance required/Monthly/Pre-run none required, post-run cleans are automated/none required/initialization is part of run setup
System offers secondary analysis software developed by instrument vendor yes
Variant report generated directly on instrument yes
Third-party analysis software available yes
Ability of software to detect mutations substitutions, indels, copy number changes
Total No. of peer-reviewed publications for this platform >1,600 for Ion sequencing
Published applications in pathology-related research >300
Fastest published turnaround time from sample to analyzed result <15 hours based on RUO platform
Lowest published variant sensitivity level .01 fresh frozen; .02 FFPE based on RUO platform
Distinguishing features of sequencer (supplied by company) setting up a sequencing run requires less than 15 minutes of hands-on time on the Ion S5 Systems; start with as little as 1 ng FFPE DNA with Ion AmpliSeq technology; sequencing run time is as few as 2.5 hours for a 1 × 200 bp sequencing run
*inclusive of sample prep, for multiple configurations, using 1 Mb and 30x average coverage per sample
Note: a dash in lieu of an answer means company did not answer question or question is not applicable
All information is supplied by the companies listed. The tabulation does not represent an endorsement by the CAP.